Abstract Background Numerous randomized trials involving acupuncture treatment for cervicogenic headache (CEH) have been conducted in recent years, but the evidence for its effectiveness is not clear. Hence, we designed a randomized trial to evaluate the efficacy and advantages of acupuncture for treating CEH. Design This is a parallel-design, two-arm, patient-assessor blinded, randomized, sham-controlled clinical trial. A total of 166 patients with CEH aged from 18 to 70 will be recruited and assigned randomly into a jin acupuncture group and a pseudo acupuncture group at a 1:1 ratio; they will receive 12 sessions of real acupuncture and sham acupuncture for 4 weeks, respectively, during the study. The primary outcomes are pain degree (PD) and pain rate (PR) calculated by the PainVision analyzer, as well as parameters detected by surface electromyography (SEMG). The secondary outcomes will be measured with the short-form McGill Pain Questionnaire (SF-MPQ), range of motion (ROM) of the neck, the Northwick Park Neck Pain Questionnaire (NPQ), the 36-item short-form Health Survey (SF-36), the Self-Rating Anxiety Scale (SAS), and the Self-Rating Depression Scale (SDS). Clinical assessments will be evaluated at baseline and in the fourth week as well as in the eighth and sixteenth weeks. Adverse events will be noted and recorded for the safety evaluation. Discussion This study will provide high-quality evidence of the value of acupuncture based on jin theory for treating CEH. Trial registration Chinese Clinical Trial Registry, ChiCTR1800015316. Registered on 22 March 2018. Updated version AMCTR-IOR-18000157. Registered on 1 April 2018.